Fix setting defalut value of needsExplicitHs

Calling script with --needsExplicitHs option erroneously set its value to False.
I have changed it to behave as expected.
Introduce a new version of is_chiral_match()

Previous version of is_chiral_match() function was design from scratch. Now it
is rewritten to utilize RDKit newly acquired ability to take stereochemistry
into account while making substructure matches.  The change rendered the
are_perm_equal() function obsolete, thus it was removed from the code too.